Analysis of nucleic acids, such as circulating cell-free nucleic acids (e.g., cell-free DNA (cfDNA) and cell-free RNA (cfRNA)), using next generation sequencing (NGS) is recognized as a valuable method for characterizing various sample types. For example, such analyses are useful as a diagnostic tool for detection and diagnosis of cancer. Current protocols for preparing a sequencing library from a cell-free nucleic acid sample (e.g., a plasma sample) typically involve isolating a single nucleic acid population, (i.e., cfDNA or cfRNA) for preparation of a sequencing library for analysis. Because only a single nucleic acid population is isolated for analysis in such protocols, precious cell-free nucleic acid material is wasted and valuable information may be lost.